Textbook-Integrated Guide to Educational Resources

TIGER

Molecular Models of DNAWilliam F. ColemanThe featured molecules this month come from the paper by David T. Crouse on the X-ray determination of the structure of DNA. Given that most students are aware of the double helix, it seems appropriate to back up a little and examine the components that give rise to this structure. Accordingly, the molecule collection includes: Purine and pyrimidine, structural precursors of the four bases found in DNA: cytosine (C), thymine (T), adenine (A), and guanine (G) The four corresponding deoxyribonucleosides The four deoxyribonucleotides (the nucleoside monophosphates) A two-base-pair fragment showing the AT and GC hydrogen-bonded complements Several small 24-base-pair DNA fragments polyAT, polyGC, and a random array of bases. The DNA fragments provide a good opportunity to have students explore features of the Jmol and Chime menus. Using the Jmol menu as an example (right-click on the structure to bring up the menu) students can use the measuring tools to get an idea of the length of a complete turn in the DNA, the relative widths of the major and minor grooves, and the diameter of the helix. They can use the coloring schemes to detect the various base pair combinations, and learn to read the code for the random sequence. In Chime they can use the Shapely coloring scheme for this same purpose. Exploring other aspects of the menu will allow students to present the molecules in the various forms, including ribbon and cartoon views. In RNA, thymine is replaced by uracil, and the sugar moiety has an axial hydroxyl group on the carbon atom adjacent to the base binding site (the 2? carbon). The structures of uracil and of uridine monophosphate are included in the molecule collection. Students can use the Web to download and examine more complex DNAs using a site such as the Nucleic Acid Database at Rutgers University.

Nucleic Acids / DNA / RNA

Molecular Models of DAPIWilliam F. ColemanThis month's Featured Molecule is DAPI (4′,6-diamidino-2-phenylindole), from the paper by Eamonn F. Healy (1). The utility of DAPI is a consequence of its being a minor-groove binder to DNA. A crystal structure of DAPI binding to the minor groove of a synthetic DNA has been determined, and the structure file made available through the RCSB Protein Data Bank (2, 3). That structure is also included in the Featured Molecules Collection, with the water molecules removed for the sake of clarity. For many students this may be their first encounter with the binding of small molecules to DNA. Another example of such binding is the intercalation of the antibiotic actinomycin into DNA. The Department of Biology at the University of Hamburg maintains an excellent Web site showing both crystal and NMR structures of actinomycin intercalation (4). Observant students will also note in the structure of DAPI a theme that has appeared several times in our Featured Molecules, and that is the non-planarity of adjacent delocalized ring systems. In DAPI, it is a five-membered ring adjacent to a six-membered ring, and the observed departure from planarity is less than that in biphenyl. Students might be asked to explain that difference.

Biomolecules (Netorials)Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David ShawBiomolecules: this is a resource in the collection "Netorials". This set of modules will provide you with a descriptive overview of the four major classes of biomolecules found in all living organisms: carbohydrates, lipids, proteins, and nucleic acids. The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.

Monomer of KevlarWilliam F. ColemanThe WebWare Molecules for July are from the paper Modern Sport and Chemistry: What a Chemically Aware Sports Fanatic Should Know by Giffin, Boone, Cole, McKay and Kopitzke.

Molecular Properties / Structure

C60; a closed shapeWilliam F. Coleman, Randall J. WildmanThe Featured Molecules for August 2002 come from the paper "Generating Closed Shapes From Regular Tilings" by Boo and Mattern. The C60 molecule shown here is an example of a closed [12P:20H] shape.

Molecular Properties / Structure

Sulfur dichloride, SCl2William F. Coleman, Randall J. WildmanThis month's molecule is sulfur dichloride, SCl2. This and other small inorganic molecules are discussed in the article by Matta and Gillespie. They describe electron density in molecules and how to analyze it to obtain information about molecular bonding and structure. Different depictions of electron density in SCl2 and other small molecules emphasize different aspects of their electron density and of the structures of the molecules.

Molecular Properties / Structure

Glycerol, HOCH2CH(OH)CH2OHWilliam F. Coleman, Randall J. WildmanThis month's molecule is glycerol. Consumers often encounter this compound labeled as glycerin, the term used for commercial applications. An ingredient in cleaning products such as soap, and toothpaste, as well as cosmetic, pharmaceutical, and food products, glycerol is one of the many chemicals that keep us clean.

Molecular Properties / Structure

Enantiomers of GuaifenesinWilliam F. Coleman, Randall J. WildmanThe WebWare molecules of the month for March are the enantiomers of guaifenesin. The synthesis of the guaifenesin racemate and of the enantiomers is described in the paper by Stabile and Dicks, "Semi-Microscale Williamson Ether Synthesis and Simultaneous Isolation of an Expectorant from Cough Tablets". Guaifenesin [3-(2-methoxyphenoxy)-1,2-propanediol] is used as an expectorant in a number of commercially available cough medicines.

Molecular Properties / Structure

Sucrose and VanillinWilliam F. Coleman, Randall J. WildmanThe WebWare molecules of the month for April relate to the sense of taste. Apple Fool, the JCE Classroom Activity, mentions sucrose and vanillin and their use as flavorings.

Molecular Properties / Structure

Shikimic AcidWilliam F. ColemanThe molecule for this month comes from the article Isolation of Shikimic Acid from Star Aniseed by Richard Payne and Michael Edmonds. Shikimic acid plays a key role in the biosynthesis of many important natural products including aromatic amino acids, alkaloids, phenolics, and phenylpropanoids. It plays such an important role that one of the key biosynthetic pathways is referred to as the shikimate pathway.

Molecular Properties / Structure

Compounds That Promote Seed GerminationWilliam F. ColemanThe two molecules for this month come from the section Compound in Smoke Provides the Spark for Germination in the article about "Research Advances" by Angela G. King. These molecules have been demonstrated to stimulate seed germination under various conditions. The butenolide moiety is frequently encountered in natural products. An interesting approach to the synthesis of such molecules can be found in this Organic Letters article (accessed January 2005).

Molecular Properties / Structure

Antimicrobial Agents Used on TextilesWilliam F. ColemanThe featured molecules of this month come from the article "Chemistry of Durable and Regenerable Biocidal Textiles" by Gang Sun and S. Dave Worley on the history and chemistry of biocidal textiles for use in the health care industry. All of these molecules can be bound to cellulose in a fabric through chemical modification, illustrating yet again the importance of such polymer-bound substrates in a wide-range of chemistries.

Molecular Properties / Structure

Molecular Models of IndicatorsWilliam F. ColemanThe article by Nicholas C. Thomas and Stephen Faulk on "Colorful Chemical Fountains" (1) reminds us that color—the colors of acid–base indicators or of metal complexes—is responsible for many of us developing an interest in chemistry. The featured molecules this month are the acid and base forms of three common indicators–phenolphthalein, methyl orange, and methyl red. These three substances display interesting structural features as the pH-induced transformation from one form to another takes place in three different ways. In the case of phenolphthalein, the lactam ring is cleaved on deprotonation to produce a carboxyl group with the concomitant removal of a proton from a phenolic group. In methyl orange, one of the nitrogen atoms is protonated in the acid form, and that proton is lost in the base form. In methyl red, a carboxylic acid function is deprotonated. There are many other interesting aspects of acid–base indicators. Since most plants and fruits contain pigments that show a color change in some pH range, it is difficult to state with any degree of certainty when these changes were first put to use in a systematic fashion. The Spanish alchemist Arnaldus de Villa Nova (Arnold of Villanova) is purported to have used litmus in the early 14th century. In general systematic use of indicators is traced to the latter half of the nineteenth century with the development of the three synthetic indicators described above. Many students will be familiar with the use of phenolphthalein to identify blood—often shown on the various forensic chemistry TV dramas by dropping some solution on a cotton swab that has been used to pick up some of the sample in question. If the swab turns red we frequently hear "It's blood". The reality of using phenolphthalein in this way is more complicated. The test is presumptive for the presence of blood, but not conclusive. It is not an acid–base reaction but rather, in the presence of hydrogen peroxide, relies on hemoglobin to catalyze the oxidation of phenolphthalein. An interesting assignment for students in a high-school or non-majors course would be to have them explore the details of this Kastle–Meyers test to see just what is involved in the correct application of the test, and what factors complicate the process. For example, would tomato juice infused with asparagus juice give a positive Kastle–Meyers test? Historically phenolphthalein was used in a variety of laxatives. Recently that usage has been discontinued due to concern about the carcinogenic nature of the substance. A review of the history of the controversy surrounding the use of phenolphthalein in laxatives would make a good research paper at the high-school level. Lastly, students with some practice building structures and performing calculations might wish to explore the structures of two other forms of phenolphthalein—one found in very acidic solutions, having an orange color, and one found in very basic solutions that is colorless.

Molecular Properties / Structure

Organic XenobioticsWilliam F. ColemanThe molecules for this month come from the article, Intermolecular Forces as a Key to Understanding the Environmental Fate of Organic Xenobiotics, by Ryan E. Casey and Faith A. Pittman. The paper describes an interesting approach to introducing students in an environmental science course, with no required chemistry background, to important questions of the ways in which molecular geometry and polarity affect the behavior of organic molecules in the environment.

Dibenzyl TerephthalateWilliam F. Coleman, Randall J. WildmanThe WebWare molecule for January is from the article "Chemical Recycling of Pop Bottles: The Synthesis of Dibenzyl Terephthalate from the Plastic Polyethylene Terephthalate" by Craig J. Donahue, Jennifer A. Exline, and Cynthia Warner. Polyethylene terephthalate from 2-liter pop bottles can be recycled by converting it to dibenzyl terephthalate.

Molecular Modeling |

Molecular Properties / Structure

Acetaminophen, Aspirin, and CaffeineWilliam F. Coleman, Randall J. WildmanThe WebWare Molecules for February are from the article, "A General Chemical Laboratory Theme: Spectroscopic Analysis of Aspirin", by Houston Byrd and Stephen E. O'Donnell. In the article, students examine non-prescription medicines containing acetaminophen, aspirin, and caffeine.

Molecular Properties / Structure |

Medicinal Chemistry

Ascorbic Acid and Methylene BlueWilliam F. Coleman, Randall J. WildmanThe WebWare molecules of the month for May are featured in several articles in this issue. "Arsenic: Not So Evil After All?" discusses the pharmaceutical uses of methylene blue and its development as the first synthetic drug used against a specific disease. The JCE Classroom Activity "Out of the Blue" and the article "Greening the Blue Bottle" feature methylene blue and ascorbic acid as two key ingredients in the formulation of the blue bottle. You can also see a colorful example of these two molecules in action on the cover. "Sailing on the 'C': A Vitamin Titration with a Twist" describes an experiment to determine the vitamin C (ascorbic acid) content of citrus fruits and challenges students, as eighteenth-century sea captains, to decide the best fruit to take on a long voyage.

Molecular Modeling |

Molecular Properties / Structure

Penicillin and Vitamin B12William F. ColemanThe WebWare Molecules for July are mentioned in the article "The History of Molecular Structure Determination Viewed through the Nobel Prizes", by Jensen, Palenik, and Suh. One of the recipients discussed, Dorothy Crowfoot Hodgkin, won the Nobel Prize in Chemistry in part for determining the structures of penicillin and vitamin B12.

Molecular Modeling |

Molecular Properties / Structure

Metal Chloride CompoundsWilliam F. ColemanThe WebWare molecules of the month for August stem from the article, "Discovery Videos: A Safe, Tested,Time-Efficient Way To Incorporate Discovery-Laboratory Experiments into the Classroom".

Molecular Modeling |

Molecular Properties / Structure

Crystal Violet, Fluorenone, and FluoreneWilliam F. ColemanThe WebWare molecules of the month for the month of September are discussed in the article by Gail Horowitz, "A Discovery Approach to Three Organic Laboratory Techniques: Extraction, Recrystallization, and Distillation". In the extraction part of the experiment, students use aqueous washes to remove a highly polar colored contaminent (crystal violet) or a nonpolar colored contaminent (fluorenone) from a desired compound (fluorene).

Molecular Modeling |

Molecular Properties / Structure

Quinine and UreaWilliam F. ColemanThe WebWare molecules of the month are discussed in two laboratory articles in this issue. Quinine is studied in the article "A Fluorimetric Approach to Studying the Effects of Ionic Strength on Reaction Rates: An Undergraduate Steady-State Fluorescence Laboratory Experiment" by Stephen W. Bigger, Peter J. Watkins, and Bruce Verity. Urea, a typical protein denaturant, is used as a cosolvent in the article "Transfer Free Energy and the Hydrophobic Effect" by Joseph M. Serafin.

Molecular Modeling |

Molecular Properties / Structure

Amylose and PolystyreneWilliam F. ColemanThe WebWare molecules of the month are amylose and polystyrene, which are examined in JCE Classroom Activity #57: "Pondering Packing Peanuts Polymers". In the activity, students investigate polymers and their chemical composition. The structures below show several repeating units of the two polymers. The helical, 50-unit amylose shows the structure that complexes with iodine to produce the blue charge-transfer complex in the starch iodine test.

Molecular Modeling |

Molecular Properties / Structure

Antiandrogen Prostate Cancer DrugsWilliam F. ColemanThese interactive images are linked to molecular structures or other graphic images from articles in our print Journal. Many articles in the Journal of Chemical Education include molecular structures naturally in a two-dimensional representation. This collection of interactive Chime-based structures are chosen from some of these molecules. While many such Web-based structure collections exist, having the structures in a single location and linked to specific articles in JCE (and vice versa) will benefit both teachers and students.

Molecular Modeling |

Molecular Properties / Structure

Fountain Pen InkWilliam F. ColemanThis months Featured Molecules are drawn from the paper Chemical Composition of a Fountain Pen by Inkby J. Martín-Gil, M. C. Ramos-Sánchez, F. J. Martín-Gil, and M. José-Yacamán on the composition and stability of inks.

Molecular Modeling |

Molecular Properties / Structure

Lubricating GreasesWilliam F. ColemanThe Featured Molecules for this month all come from the paper "Lubricating Grease: A Chemical Primer" by Craig Donahue. This paper is a rich source of structural examples ranging from small molecules to metal complexes to polymeric species.

Molecular Modeling |

Molecular Properties / Structure

The Chemistry of Popcorn; Polymers of GlucoseWilliam F. ColemanThe featured molecules this month are all polymers of glucose, and relate to the two papers on the chemistry of popcorn: "Popping Popcorn Kernels: Expanding Relevance with Linear Thinking" by Jordan L. Fantini, Michael M. Fuson, Thomas A. Evans, and "Popcorn What's in the Bag?" by Marissa B. Sherman and Thomas A. Evans.

Molecular Modeling |

Molecular Properties / Structure

Catalysts from the 2005 Nobel Prize in ChemistryWilliam F. ColemanThe 2005 Nobel Prize for Chemistry celebrated molecules that are of great value to researchers, to the broader society, and to chemical educators. Some of those molecules are featured here.

Molecular Properties / Structure |

Molecular Modeling

The Chemistry of Highly Fluorinated CompoundsWilliam F. ColemanThe featured molecules for January come from the paper Fluorous Compounds and Their Role in Separation Chemistry by Maria Angeles Ubeda and Roman Dembinski. This paper explores the use of highly fluorinated compounds as solvents, catalysts, and reagents.

Molecular Modeling |

Molecular Properties / Structure

Perfume Chemistry; Jasmone, α-Damascone, Geraniol, Civetone, and Musk BaurWilliam F. ColemanThe featured molecules for the month of January are some of the natural and synthetic molecules used to create perfumes. The chemistry of perfumes is discussed in the article "Chemistry Perfumes Your Daily Life". Jasmone is a natural component of jasmine and a key component for its odor; α-damascone is a natural component of rose oil; geraniol is a synthetic rose odor; civetone is a macrocyclic musk that used to be obtained from the civet cat; and musk baur is a synthetic molecule with a musky smell.

Molecular Modeling |

Molecular Properties / Structure

Polycyclic Aromatic HydrocarbonsWilliam F. ColemanThe featured molecules for the month of February are a number of polycyclic aromatic hydrocarbons (PAHs) discussed in the article "Fluorescence, Absorption, and Excitation Spectra of Polycyclic Aromatic Hydrocarbons as a Tool for Quantitative Analysis". PAHs are ubiquitous in air, soils, and water as a result of both direct and indirect emissions. PAHs are discharged into environments as byproducts of the combusion of fossil fuels used for transportation and generation of electricity. Other sources of PAH emissions include industrial processes, biomass burning, waste incineration, oil spills, and cigarette smoke.

Molecular Modeling |

Molecular Properties / Structure

Bioorganic Synthesis; Monosodium Glutamate and Other Amino AcidsWilliam F. ColemanThe March featured molecules are discussed in the article "The Monosodium Glutamate Story: The Commercial Production of MSG and Other Amino Acids". This paper provides a number of opportunities for introducing students to the importance of stereochemistry in bioorganic synthesis. The collection here includes all of the relevant molecules in the synthesis of α-amino-ε-aminocaprolactam (ACL). The introduction of two chiral centers in the reaction of cyclohexene with NOCl results in four diastereomers, and it is instructive to ask students to predict the relative abundance of those isomers and the dependence of that distribution on the extent to which the reaction is syn- or anti-addition, and to account for the fact that the resultant oxime, and the ACL, are obtained as racemates.

Molecular Modeling |

Molecular Properties / Structure

The Big Picture; A Classroom Activity for Organic ChemistryWilliam F. ColemanIn the article "The Big Picture: A Classroom Activity for Organic Chemistry", Thomas Poon makes interesting use of the device exploited by Istvan Banyai in his Zoom books to help students of organic chemistry make connections between the molecular world and ways in which those molecules are important in daily life. The paper should have appeal at all levels of science education from the time the idea of molecules is first introduced through college-level courses. Along the way, students will encounter important biological molecules (such as chlorophyll), inks (such as pen ink), CFCs, hydrocarbon fuels, plastics (such as Lexan polycarbonate), and molecules with medical applications (such as aspirin and novocaine).

Molecular Modeling |

Molecular Properties / Structure

Boron ClustersWilliam F. ColemanThe May featured molecules are discussed in the Viewpoints article "Boron Clusters Come of Age". The review paper by Russell N. Grimes on boron clusters reminds us both of the past impact that these interesting structures have had on the development of our understanding of cluster chemistry and on the future development of what one might refer to as "post-fullerene" clusters. The wide range of structures found in this paper admirably illustrate the structural flexibility arising from clusters of a variety of symmetries and degrees of boron replacement with carbon and other atoms.

Molecular Modeling |

Molecular Properties / Structure

Enantiomer Specificity in PharmaceuticalsWilliam F. ColemanThe molecules of the month this month come from three papers: Demonstration of Enantiomer Specificity of Proteins and Drugs by Gretchen L. Anderson, Incorporation of Medicinal Chemistry into the Organic Chemistry Curriculum by David C. Forbes, and Infusing the Chemistry Curriculum with Green Chemistry Using Real-World Examples, Web Modules, and Atom Economy in Organic Chemistry Courses by Michael C. Cann and Trudy A. Dickneider.The authors of these papers use molecules whose names at least are familiar to the majority of students to introduce important structural and synthetic concepts. A particularly poignant example is that of thalidomide, in which the two enantiomers produce dramatically, and in the case of the S form tragically, different results. In addition to demonstrating enantiospecific reactivity, the thalidomide case is a good starting point for a discussion of how chemists ask questions, what questions we should be asking, and whether or not it is possible to minimize, if not completely eliminate, unintended consequences.

Molecular Modeling |

Molecular Properties / Structure

Chocolate; Theobromine and CaffeineWilliam F. ColemanThe featured molecules this month come from "Chocolate: A Marvelous Natural Product of Chemistry" by Ginger Tannenbaum. As discussed in the article, chocolate is a natural food and is a mixture of many chemical compounds; approximately 400 compounds have been identified in chocolate following fermentation and processing. During processing, a liquid called "chocolate liquor" is formed that is composed of about 55% fat, 17% carbohydrate, 11% protein, and most of the remainder is tannins and ash. Depending on its source, it may also contain theobromine, an alkaloid related to caffeine, in quantities ranging from 0.8% to 1.7%. Caffeine is found in lesser quantities. Theobromine and caffeine are both methyl-xanthines. Theobromine is a smooth muscle stimulant, while caffeine is predominately a central nervous system stimulant. When solidified, the liquor forms bitter (unsweetened) cooking or baking chocolate.

Molecular Modeling |

Molecular Properties / Structure

Alkaloids; Strychnine, Codeine, Heroin, and MorphineWilliam F. ColemanThe featured molecules this month come from the article "The Conversion of Carboxylic Acids to Ketones: A Repeated Discovery" by John W. Nicholson and Alan D. Wilson. The authors describe the repeated discovery of this reaction and illustrate its central role in Woodward's total synthesis of strychnine. Strychnine is a member of a large class of nitrogen heterocycles known as alkaloids, a name derived from the fact that all produce basic solutions in water. Other well-known members of this class of compounds, all of which are pharmacologically active, are nicotine, atropine (deadly nightshade), quinine, lysergic acid, cocaine, and the three structurally similar compounds codeine, heroin, and morphine.

Molecular Modeling |

Molecular Properties / Structure

Chemistry of Blood TypeWilliam F. ColemanThe molecules for this month come from the paper Glycosyltransferases A and B: Four Critical Amino Acids Determine Blood Type by Rose, Palcic, and Evans on structural factors determining blood type. Included are interactive molecule files for the three determinant molecules and the two donors.

Molecular Modeling |

Molecular Properties / Structure

Azulene ChemistryWilliam F. ColemanThe month's featured molecules come from the paper An Azulene-Based Discovery Experiment: Challenging Students To Watch for the "False Assumption" by Charles Garner illustrating some of the chemistry of a substituted azulene. Azulene is a structural isomer of naphthalene and differs from it in several important ways, the most obvious being azulene's intense blue color, which arises from the S0 → S2 transition. Another unusual feature of this molecule is that its fluorescence arises from the reverse of this transition rather than from S1 → S0.

Molecular Modeling |

Molecular Properties / Structure

Menthol SteioisomersWilliam F. ColemanThe JCE Featured Molecules for July come from the paper An Engaging Illustration of the Physical Differences among Menthol Stereoisomers by Edward M. Treadwell and T. Howard Black on the use of commercially available stereoisomers of menthol to illustrate properties of enantiomers and diastereomers. The paper describes the use of four of the eight possible stereoisomers. Structures of all eight stereoisomers are included in this month's molecule collection, labeled by the chirality of the three chiral atoms. In addition to the exercises described in the paper, students can be asked to match the appropriate structures to those shown in the paper, or to generate structures for the isomers that are not discussed.

Molecular Modeling |

Molecular Properties / Structure

Weekly Molecules; A Cure for the 830 a.m. BluesWilliam F. ColemanThe concept of an online molecule of the time period, day, week, or month, as in the case of this column has increased in popularity since the initial Web sites created at a number of British universities in the mid-1990s. The paper, 8:31 a.m. Belly Flop: Attitude Adjustment through Weekly Feature Molecules by Sonya Franklin, Norbert Pienta, and Melissa Fry describes a study of student responses to a molecule of the week program. Some of the results from their surveys of students indicate that the program indeed helps students place the chemistry that they are learning into a broader societal context. Visualizing these molecules in three dimensions helps students who have difficulty going from the two-dimensional drawing to the details of structure and stereo-chemistry. Some of the recent controversy that followed the now infamous comments by Harvard President Lawrence Summers, brought up, once again, the debate over whether men and women have different abilities to visualize in three dimensions. Many of us have seen a lot of evidence that such a difference is not necessarily gender based, but we should be focusing attention on ensuring that such differences are not determining factors for students' success in science. At one time students who could not titrate well were discouraged from becoming chemists. We should make certain that we are not discouraging students for equally unimportant reasons.

Molecular Modeling |

Molecular Properties / Structure

Molecular Model of Creatine SynthesisWilliam F. ColemanThe featured molecules for this month come from the paper Creatine Synthesis: An Undergraduate Organic Chemistry Laboratory Experiment by Andri Smith and Paula Tan on the synthesis of creatine in introductory organic chemistry. This synthesis is sufficiently straightforward to be used in non-majors and general chemistry courses. The structures illustrate some of the limitations associated with the computation of molecular structure. The two adenosine phosphates ADP and ATP exhibit a large number of conformations due to rotation of the adenine system around the bond to the ribose ring, multiple rotational conformations in the phosphate groups, the ionic state of the compound, and the interaction with the solvent or another species such as creatine. The structures that are given for ADP and ATP are derived from PM3MM calculations and are very similar to those derived using the UFF force field. Sarcosine, creatine, and creatine phosphate were treated using the model chemistry B3LYP/6-31+G(d). Perhaps the most interesting structural feature is found in the small molecule cyanamide. Observant students might notice in the Web-based structure that the NCN grouping in cyanamide is non-linear, with an angle of about 177°. This is found for essentially all levels of theory we examined up through the G2 combined model. For students who do notice this deviation from linearity it is useful to ask them whether they are surprised, ask them to defend their answer, send them to the literature to see whether such behavior is seen for cyanamide in other phases (it is), and finally to speculate on possible explanations for the observed non-linearity.

Molecular Modeling |

Molecular Properties / Structure

Parallel Combinatorial Synthesis of Azo DyesWilliam F. ColemanThe featured molecules for this month are from "Parallel Combinatorial Synthesis of Azo Dyes: A Combinatorial Experiment Suitable for Undergraduate Laboratories" by Benjamin W. Gung and Richard T. Taylor. The principle of combinatorial chemistry is illustrated by generating a relatively large number of colorful dyes using only one common reaction, the diazo coupling, and two common reactants with small variations. Fully manipulable (Chime) versions of these molecules appear below.

Copper and Nickel Complex IonsWilliam F. ColemanThe Featured Molecules this month come from Donald C. Bowmans article A Colorful Look at the Chelate Effect, the final Overhead Projector Demonstrations column edited by the late Doris Kolb. Included in the online collection are all eight isomeric forms of [Ni(en)3]2+, demonstrating the effects of ligand backbone conformation.

Molecular Modeling |

Amino Acids |

Molecular Properties / Structure

Amino AcidsWilliam F. ColemanThe Featured Molecules this month are the 20 standard α-amino acids found in proteins and serve as background to the paper by Barone and Schmidt on the Nonfood Applications of Proteinaceous Renewable Materials. The molecules are presented in two formats, the neutral form and the ionized form found in solution at physiologic pH.

Molecular Modeling |

Amino Acids |

Molecular Properties / Structure

Luminescent Molecular ThermometersWilliam F. ColemanThe Featured Molecules this month come from the paper "Luminescent Molecular Thermometers" by Uchiyama, Prasanna de Silva, and Iwai exploring the many ways that photophysical properties can be used as temperature probes. They introduce a variety of molecule types, many of them now in our molecule collection. Excited states play a central role in this paper and it provides an opportunity to introduce students to some excited state properties.

Molecular Modeling |

Molecular Properties / Structure |

Photochemistry

Microwave-Assisted Heterocyclic ChemistryWilliam F. ColemanThe featured molecules for this month come from the Green Chemistry article, "Microwave-Assisted Heterocyclic Chemistry for the Undergraduate Organic Laboratory" by Musiol, Tyman-Szram, and Polanski.

Molecular Modeling |

Molecular Properties / Structure |

Heterocycles

Coumarin, Naphthalene, and Additional Polycyclic Aromatic HydrocarbonsWilliam F. ColemanThe featured molecules this month are drawn from two papers. The first, "One-Pot Synthesis of 7-Hydroxy-3-carboxycoumarin in Water", is a Green Chemistry feature by Fringuelli, Piermatti, and Pizzo. The three-dimensional versions of the molecules in the synthesis of the coumarin derivative are directly tied to the reaction scheme included in the paper, opening the possibility of showing large numbers of complex synthetic pathways in this manner.The second paper is "Determining the Carbon-Carbon Distance in an Organic Molecule with a Ruler" by Simoni, Tubino, and Ricchi. This article describes an experiment to determine the size of a naphthalene molecule, using an extension of classic experiments for determining molecular size and Avogadro's number. While the structure of naphthalene will come as no surprise to most students, the molecule collection also includes additional polycyclic aromatic hydrocarbons (PAHs) that can be used to introduce students to the environmental and health issues related to these molecules.

Molecular Modeling |

Molecular Properties / Structure |

Aromatic Compounds

Moth Repellent ChemicalsWilliam F. ColemanThe featured molecules this month come from the paper The chemistry of moth repellents by Gabriel Pinto. Several of the molecules exhibit interesting structural features that students should explore. Hexachloroethane, not surprisingly, has energy minima in the staggered form that is shown. Students could be asked to look at the models for empenthrin and permethrin to see if they can see similar staggered arrangements in these more complex molecules. Camphor is a good way to introduce strained structures, and students can use the Jmol version of the model to measure bond angles to see if they can identify some of the consequences of this strain. The carbonyl moiety in camphor is interesting as it is non-planar.

3D Molecular Symmetry Shockwave; A Web Application for Interactive VisualizationNickolas D. Charistos, Constantinos A. Tsipis, Michail P. Sigalas3D Molecular Symmetry Shockwave is a Web-based application for interactive visualization and three-dimensional perception of molecular symmetry. The user interface is simple, and students learn how to use the program from the built-in help screens. The animation uses the Macromedia Shockwave browser plug-in, and requires a download of only 256 KB, allowing it to be used even with low bandwidth Internet connections. Its performance is comparable to a desktop application.

Crystals / Crystallography |

Group Theory / Symmetry |

Molecular Properties / Structure |

Thermodynamics

Close Packing of Layers of SpheresWilliam F. ColemanAn animation of the close packing of layers of spheres. In this version, clicking on text links adds the second and third layers, with two options for the third layer. After both ways of adding the third layer have been explored the user has an option to go to a second version that has no text but rather allows the user to drag the layers over one another.

Crystals / Crystallography |

Molecular Properties / Structure |

Solids |

Enrichment / Review Materials

An Animated Interactive Overview of Molecular SymmetryMarion E. Cass, Henry S. Rzepa, David R. Rzepa, Charlotte K. WilliamsAn Animated Interactive Overview of Molecular Symmetry is a series of Web pages designed to help instructors teach molecular symmetry. These pages combine interactive Jmol images and instructional text that allow students to examine and explore the operations and elements that give rise to molecular symmetry.

Crystals / Crystallography |

Group Theory / Symmetry |

Molecular Properties / Structure |

Thermodynamics

JCE Featured MoleculesWilliam F. Coleman, Randall J. WildmanThese interactive images are linked to molecular structures or other graphic images from articles in our print Journal. Many articles in the Journal of Chemical Education include molecular structures naturally in a two-dimensional representation. This collection of interactive Chime-based structures are chosen from some of these molecules. While many such Web-based structure collections exist, having the structures in a single location and linked to specific articles in JCE (and vice versa) will benefit both teachers and students. In addition to static images, two fully manipulable versions (Jmol, MDL Chime) of these molecules are available.

Molecular Modeling |

Molecular Properties / Structure |

Enrichment / Review Materials

A Graphical User Interface for PC GAMESSWayne P. AndersonGAMESS is a set of computational chemistry tools available free for several computing platforms. Using the set of tools described here along with the pcgRun tool provided allows these tools to be used on the ubiquitous Windows PC with a graphic interface preferred by many of us over the command line.

Computational Chemistry |

Molecular Properties / Structure |

Undergraduate Research |

Enrichment / Review Materials

HCP LayersWilliam F. ColemanAn animation showing both the top and side views when three layers of spheres are arranged in a hexagonal close-packed array The user can control the animation through vcr controls.

Mechanisms That Interchange Axial and Equatorial Atoms in Fluxional ProcessesMarion E. Cass, Henry S. Rzepa, King Kuok HiiThe Berry pseudorotation is a classical mechanism for interchanging axial and equatorial ligands in molecules with trigonal bipyramidal geometry. Teaching this mechanism presents particular pedagogic problems due to both its dynamic and three dimensional character. The approach taken here illustrates these processes using interactive animations embedded in a Web page and overcomes many limitations of a printed page.

Computational Chemistry |

Molecular Properties / Structure |

Nonmetals |

Enantiomers |

NMR Spectroscopy |

Mechanisms of Reactions |

Molecular Mechanics / Dynamics

Mage; A Tool for Developing Interactive Instructional GraphicsStephen F. PavkovicMage is a graphics program especially well suited for visualizing three-dimensional structures of proteins and other macromolecules. It is an important tool for biochemists and finds many applications in biochemistry courses. We utilize Mage to create interactive instructional graphics of potential use in a wider range of undergraduate chemistry courses, and present some of those applications here.

Characteristics of MaterialsAmerican Chemical SocietyWhat makes diapers absorbent? Is peanut butter stickier than syrup or jelly? Strong, stretchy, sticky, or sweet—everything around us has special properties which make them unique. See if you can identify and compare the characteristics of materials.